As I understand it, the main purpose for using secondary fermentation is to allow the fermentation to continue longer while getting the beer off of the trub before it starts to break down. Once the beer is primed and bottled, I have noticed a dramatic improvement in the taste if the bottles are aged for at least two weeks.

What I'm wondering is, what is the difference between racking to a secondary fermenter to allow fermentation to continue and bottle-aging (where you allow fermentation to continue in the bottle). The two differences that strike me are the priming sugar (which is not present in the secondary fermenter) and the volume of the fluid (2-1/2 gallons versus 22 oz).

The term "secondary fermentation" is something of a misnomer. The beer should be finished or nearly finished fermenting when racked to secondary. The primary reason for secondary fermentation is your second point: to get the beer off the yeast and trub and let it clear and condition.

As you have discovered, many beers (but not all) benefit from some aging. This can be done in the bottle as well as in a secondary fermenter, but the evidence is that it is more effective if done in bulk in secondary.

LG, I generally let my beer sit in the secondary for a good long while (months for higher gravity beers and 1 month for lower gravity beer). My feeling is that the aging/mellowing you get in the bottle is relatively the same as you get from a prolonged secondary. The advantage to the bottle aging is that you free up your secondary.

Try brewing an Ale with a strong hops backbone and let it sit in the secondary for a month or so and you will see that the hop bite will mellow just the same as if you bottled and let them sit in the coat closet for a month.

Back before I got into kegs, I used to "lager in the bottle." That is, after primary fermentation was over, I'd transfer the beer directly into bottles, let them sit a week in the basement to carbonate, then put them in the fridge to lager. My reasoning was the more yeast available to lager the beer, the quicker (and better) the lagering process. This approach alway left a thicker but compact yeast cake in the bottle, and to tell the truth, the results were just as good as lagering in the keg.

Other than that, I use a secondary for all my beers prior to bottling/kegging.

Thanks to everybody for your replies. I've learned from you all, as usual. The point about the yeast cake in the bottles is right on. One of the things I notice about the batches that I used secondary fermentation with was that there was very little yeast in the bottle as compared with my initial batches that were bottled after a week in primary. The yeast always does a good job of sticking to the bottom, however, so I never have trouble with pouring.

Concerning protein haze, my limited experience is that my beers seemed to clear more quickly in bottles than in a carboy. Might be something to do with more surface area of the container per volume of beer when in a bottle vs. carboy.

I screwed up the experiment. I had split a 5-gallon kit from Midwest into two batches. Batch 1 was primaried for a week and secondaried for two weeks. Batch 2 was primaried for two weeks then bottled. However, it won't be fair to compare them because I used different water for each batch. For the first, I followed my usual practice of using Abita Springs water. For those who do not know, this is the same water used in Abita beer, a local microbrewery. For the second batch, I ran out and didn't want to make a trip to the grocery store because I was squeezing in a brewing session while the baby was napping. I used tap water. Nothing against tap water; I drink it all the time, but I know from past experience that my beer (as well as coffee & tea) tastes better with spring water.